R Notebook

Introduction to the snow vole dataset

For these exercises we will use some published data, freely available from the Dryad repository: Bonnet, T & Postma, E (2018). Data from: Fluctuating selection and its (elusive) evolutionary consequences in a wild rodent population. Dryad Digital Repository. https://datadryad.org//resource/doi:10.5061/dryad.6767m.

For some context, these data are from the long-term monitoring of a population of snow voles (Chionomys nivalis) in the Swiss Alps.

A young snow vole. Picture by T. Bonnet

We will use only the file “Phenotypic data” or “YearPheno.txt”.

What exactly the variables are is not crucial, but will help make sense of the exercises:

• ID: focal individual unique identifier
• animal: duplicate of ID to fit relatedness matrices in animal model
• Mother: mother of the focal individual
• Year: year of measurement
• Sex: Female or male
• Age: Juvenile or adult
• BMI: Body mass index. Check the publication for details
• RJst: Standardized relative Julian day
• RJ2st: Squared Standardized relative Julian day
• Phi and PhiZ: survival to the next year (duplicated for historical reasons)
• RhoZ: reproduction on the next year
• FitnessZ: RhoZ + 2Phi. Check the publication for details
• GGImm: proportion of assumed immigrant ancestry used to fit genetic groups. Check the publication for details
• BMIst: BMI standardized within years
• BMI1 and BMI2: BMI in years of positive or negative selection.

Understanding the data

Linear models

Generalized linear models

Mixed models

Generalized linear mixed models